In addition to the Kansas trH3N2 sequences from Kansas State
University, the USDA released the missing genes (PB2, PB1, PA, NP, NS)
from the two 2010 Iowa trH3N2 isolates, A/swine/Iowa/A01049035/2010
and A/swine/Iowa/A01049034/2010,
and all five gene segments were of trH3N2 swine origin. Thus, the two
Iowa isolates have the same constellation of genes as H3N2pdm11, which
is in all 10 of the human cases as well as the swine isolate from New
York, A/swine/NY/A01104005/2011.

The Iowa sequences are easily distinguished from H3N2pdm11 because only
the NP gene segment matches. These data indicate that the
constellation H3N2pdm11 alone does not generate a high frequency of
human cases because all H3N2pdm11 isolates not only share the same
constellation, but the lineage of all 8 gene segments match.

Thus, the latest series of newly released sequences highlight the low
frequency of H3N2pdm11 in swine, which remains limited to New York
isolate identified from a Sept 13 collection. The failure to find any
matches in swine isolates prior to the first human cases continues to
support H3N2pdm11 sustained spread in humans, leading to matches in 10
of 10 human cases and only one match in a collection after the spread
in humans.

The November
22 “Have You Heard?" cites matches in “multiple states” and Nancy
Cox is reported to have said there was a match in pigs in the “US
Midwest”, which may represent as little as one unreported outbreak,
which would represent “multiple states” since the New York match was
not in the Midwest. This match has not been reported, but the
number of cases appears to be limited and increasingly likely to have
happened after H3N2pdm11 accelerated spread in people.